I'm installing a new trolling motor on the boat but I wanted to get yalls input on if I should mount directly to the boat or use some rubber between the trolling motor mount and top cap of the boat?

definitely use a semi rigid rubber mat under it. It will help it stay tight and also help control noise.

.....at least for my boat.

Before I would have to tighten the bolts once a month or so and I always knew when it was time to do so because of the "clacking" noise it would make. Since I added a hard rubber cushion underneath it it hasn't had to be retightened since. HA....now all I have to tighten is the bolts on the cradle itself. Even blue loctite doesn't seem to help mine in that regard.

Also, the rubber pad will help a little with the gel coat. In the event that you change again in the future, the gel coat will not be nearly as scratched up.